Rory is delighted when Headmaster Hanlin Charleston from her old prep school asks her to host a young student, Anna, who is thinking of applying to Yale. However, Anna is much more interested in boys than academics and runs off to party, leaving Rory to deal with Logan’s elaborate practical jokes. Meanwhile, Lorelai and Luke have their first argument when she upsets him by buying an old boat that had previously belonged to his father.
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After 19-year-old Rory Gilmore makes love with her former boyfriend, Dean--who is married--she argues bitterly with Lorelai, who is disappointed by her daughter's choices. Despite her best efforts, Rory cannot resist Dean, even when she guiltily observes how hard Dean's eager young wife is working to keep their marriage together.
While calling Lorelai from Rome, Rory admits that she complicated her relationship with Dean. Lorelai gives Dean a letter from Rory, but Dean's wife, Lindsay, finds the letter and makes Dean move out of the house. Rory returns from Europe, and a terrible argument ensues when she and Lorelai encounter Lindsay and her mother. Meanwhile, Luke returns to Stars Hollow after spending several weeks helping his injured sister, Liz, on the Renaissance Fair circuit. Luke and Lorelai try to find a private spot to say hello but are interrupted by a town parade.
Early in the morning after Lorelai and Luke spend a romantic night together at Luke's place, Lorelai walks into the diner dressed in one of Luke's flannel shirts and discovers that the place is full of customers. Lorelai is a little offended when it appears that no one cares about their relationship--until it becomes a topic of heated discussion at the town meeting. Meanwhile, Rory verbally spars with a haughty, rich student named Logan after he is rude to her friend Marty. And Paris holds a wake for her older lover Professor Asher Flemming, who died over the summer.
Rory and Dean have difficulty meeting alone because they live far apart and Dean shares a car with his estranged wife. Impulsively, Rory asks Dean if he left his wife because Lindsay found Rory's letter--and she is not completely satisfied with his response. Lorelai and Sookie manage Jackson's campaign when he decides to compete against Taylor for town selectman. Lane tells her band mate Zach that she has feelings for him.
Feeling bad that her relationship with Dean has become awkward, Lorelai suggests that she and Luke go on a double date with Rory and Dean. But Lorelai's plans go awry when Luke is unable to disguise the fact that he thinks Dean isn't good enough for Rory. Meanwhile, Emily and Richard are lonely and a little lost without each other, but neither one can take the first step toward reconciliation.
Lorelai and Sookie are thrilled when author Norman Mailer (himself) and a young reporter, Josh Davies, show up repeatedly in the dining room of the Dragonfly Inn, but Sookie's awe turns to annoyance when Mailer refuses to order any food. Working on a story for the Yale newspaper, Rory uncovers evidence of an intriguing secret society to which Logan belongs. Meanwhile, when Rory's father, Christopher, appeals to Lorelai for help after his girlfriend leaves him to raise their baby daughter by himself, Rory orders him to leave Lorelai alone. Finally, Sookie realizes that she is pregnant again.
Rory is impressed when Logan takes her to an elaborate event staged by his secret society, and she participates in a thrilling--but dangerous--stunt. Meanwhile, when she discovers that Lorelai is dating Luke, Emily insists he come to dinner. Not to be outdone, Richard invites Luke to a game of golf, and Luke is overwhelmed by the strength of the elder Gilmores' personalities.
Rory is honored when Emily and Richard give a party to introduce her to their Yale alumni friends, but it soon becomes obvious that their ulterior motive is to find her a suitable husband. When Dean arrives at the party to pick Rory up, he realizes he doesn't belong in her privileged world. Meanwhile, Luke cooks a romantic dinner for Lorelai, but their evening is interrupted by newlyweds Liz and T.J., who are feuding.
Rory decides that she and Lorelai should split up at the next Friday night dinner and confront Richard and Emily separately about ending their separation. However, Emily dashes their hopes of a reconciliation by announcing that she is ready to begin dating. Meanwhile, Lorelai invites Christopher for lunch at the inn, unaware that Rory had warned Christopher to stay away from her mother. Feeling guilty that she hadn't told Luke about seeing Christopher, Lorelai confesses that they had lunch, and Luke tries to convince himself that he isn't jealous.
Rory is delighted when Headmaster Hanlin Charleston from her old prep school asks her to host a young student, Anna, who is thinking of applying to Yale. However, Anna is much more interested in boys than academics and runs off to party, leaving Rory to deal with Logan's elaborate practical jokes. Meanwhile, Lorelai and Luke have their first argument when she upsets him by buying an old boat that had previously belonged to his father.
Wanting to make peace with Rory, Christopher visits her at Yale, but she rejects his attempt at reconciliation. When Lorelai learns that Christopher's father died, she spends an evening at his home trying to console him but neglects to tell Luke the truth about where she was. Meanwhile, Emily and Richard are briefly reunited when they rescue a lost dog. Luke brings Lorelai her own portable skating pond. And the annual Stars Hollow Revolutionary War reenactment takes on a racy new twist.
Rory offers to help Logan write an article for the Yale Daily, but she is disappointed when he doesn't invite her to be his date at a book-signing party hosted by his father. When Richard sees Emily talking to a man she dated, he rear-ends her car, forcing her to ride home with him. The elder Gilmores reconcile and decide to renew their wedding vows. Meanwhile, Emily warns Christopher that Lorelai and Luke are getting serious, and he had better do something quickly if he hopes to end up with Lorelai.
In the series' landmark 100th episode, Lorelai and Rory feel obligated to give Emily a bachelorette party on the night before Richard and Emily renew their marriage vows. At the ceremony the following day, Rory tells Logan she wants a relationship with him even though he's not ready to commit. Later, when Lorelai, Luke and Christopher discover Rory and Logan together, half-dressed, the shocking scene leads to an angry confrontation between Luke and Christopher. A furious Lorelai figures out that Emily invited Christopher in an attempt to destroy Lorelai's relationship with Luke.
After the disastrous scene at her parents' marriage recommitment ceremony, Lorelai begs Luke not to give up on their relationship. However, Luke's decision that he needs time alone leaves Lorelai devastated. Stranded at Yale without her car and worried about Lorelai's depressed state, Rory borrows Logan's limousine and driver and travels home to Stars Hollow to care for her mom. Meanwhile, Taylor goads the town residents into taking sides on the Lorelai/Luke relationship.
Already upset that she and Luke ended their relationship, Lorelai feels even worse after she discovers that Luke's boat is no longer in her garage. Knowing that Lorelai is the costume designer for the elementary school's production of "Fiddler on the Roof," Luke agrees to build sets in hopes of seeing her. Meanwhile, Rory and Marty plan to spend a day together, but Logan stops by Rory's dorm room and convinces them to go out to dinner with him. After a terrible evening with Logan's clique, Marty tells Rory how much he likes her, but she admits she really likes Logan.
Richard and Emily return from their second honeymoon, and Rory attends the customary Friday night dinner. But an angry Lorelai refuses to see or speak to Emily. Rory surprises everyone with a rare outburst directed towards her grandmother for interfering in Lorelai's love life. Miserable without Lorelai, Luke gets into a dark mood that causes him to burn food and throw any customer who complains out of the diner. Emily unexpectedly visits the diner to talk to Luke. Meanwhile, Lane is horrified when she realizes that her mother has more influence over her than she thought.
After seeing Logan on a date with another girl, Rory regrets their new agreement to date other people. Later, Rory attends a party with Logan's friend Robert, forcing Logan to admit his jealousy. Meanwhile, now that Lorelai and Luke are happily reunited, Emily can't understand why Lorelai still refuses to come to Friday night dinner. Emily's second visit to speak with Luke at the diner leads to a bitter mother/daughter confrontation. Finally, Michel appears on the game show "The Price is Right" and wins a motor home.
When Stars Hollow's oldest resident dies and leaves his house to the town, Luke has an ulterior motive for volunteering to help turn the house into a temporary museum. Dean is also working on the project and offers Luke unwelcome advice about the dangers of dating a Gilmore girl. To get publicity for the Dragonfly Inn, Lorelai grants an interview with a travel magazine but immediately regrets the unkind comments she makes about being raised by Emily. Meanwhile, Lane suspects that Zach is having an affair with music store owner Sophie, while Rory and Paris are both devastated by trouble with their respective boyfriends.
Rory tells Logan that she can't have a casual romantic relationship with him, and they should return to just being friends. But Logan surprises Rory by insisting he's ready to commit to her. However, when Logan brings her home to meet his powerful and intimidating family, Rory is shocked by his parents' negative reaction to the relationship. The following day, Logan's father, Mitchum Huntzberger, apologizes to Rory and offers her an internship at one of his newspapers. Meanwhile, when Sookie is placed on bed rest by her doctor, Lorelai asks Luke to fill in as the substitute chef at the Dragonfly Inn.
Wanting to make a good impression with Logan's powerful father, Mitchum Huntzberger, Rory learns everything she can about him before starting work as an intern at one of his newspapers. When Lorelai discovers that Emily and Richard have invited Logan to Friday night dinner, she ends her boycott of family gatherings in order to get to know Logan better. During the evening, Emily and Richard fawn over Logan, but Lorelai sees a side of him that causes her to worry about Rory's involvement with the Huntzberger family. Meanwhile, Lorelai gets an interesting job offer, and Luke tries to persuade Taylor to close the Stars Hollow museum.
Rory is surprised by the performance review she receives at the newspaper from Logan's father, Mitchum Huntzberger. Luke's plan to buy the Twickham house is threatened when Kirk makes a competing bid. Lorelai is thrilled when the travel magazine featuring The Dragonfly Inn appears on newsstands but worries about Emily's reaction to the article. Meanwhile, Sookie begins to have contractions and will soon deliver her baby. And Emily sponsors a ballet dancer.
After spending a night of reckless behavior with Logan, Rory is rescued by her mother. But Lorelai is shocked to hear her daughter's plans for the future. Lorelai first asks Richard and Emily for help but soon realizes that Luke is the only person she can trust.